Tag: Genetics

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Wanted: A million genomes for precision medicine

Eric Dishman
Eric Dishman, director of the All of Us Research Program at the National Institutes of Health, meets the press at the University of Washington. (GeekWire Photo / Alan Boyle)

Eric Dishman is a living, breathing advertisement for the ambitious experiment he’s in charge of, the National Institutes of Health’s “All of Us” drive to collect and analyze the genomes of a million Americans.

If it weren’t for the fact that he had his genome sequenced seven years ago, he probably would not be living and breathing.

Back then, he was struggling with a rare form of kidney cancer that had put him through decades’ worth of chemotherapy, radiation and misery. And the end was near.

“I was probably going to die, and I was literally on my last business trip to both Boston and San Diego, where a lot of the early genomics work was being done,” Dishman, a former Intel executive, recalled today during a sit-down with journalists at the University of Washington.

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Unscrambling the tale of an astronaut’s genes

Mark and Scott Kelly
Retired astronauts Mark Kelly and Scott Kelly are still identical twins. (NASA Photo / Robert Markowitz)

My Twitter feed was buzzing this week with reports that Scott Kelly’s genes were knocked permanently out of phase because he spent a year in space.

Some of the reports made it sound as if Scott Kelly was no longer the identical twin of retired astronaut Mark Kelly, who participated in the genetic study down on Earth.

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DNA sequencer in space solves a mystery

Peggy Whitson with DNA secquencer
NASA astronaut Peggy Whitson performed the Genes in Space-3 investigation on the International Space Station using devices that amplify and sequence microbial DNA samples. (NASA Photo)

NASA isn’t saying it’s aliens — but the space agency is touting its ability to identify organisms using the first DNA sequencer in orbit.

Oxford Nanopore Technologies’ palm-sized MiniON sequencer was sent up to the International Space Station last year, and it’s now been paired up with a DNA replicator that’s able to amplify genetic samples through a process known as polymerase chain reaction, or PCR.

Together, the devices were employed to check bacterial samples as part of an experimental campaign called Genes in Space-3.

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Semi-synthetic bacteria make ‘alien’ protein

Semi-synthetic bacteria
Bacteria express a green fluorescent protein that’s produced from DNA instructions with unnatural chemical “letters” added. (Scripps Research Institute Photo / Bill Klosses)

Researchers have reached a new milestone in their effort to expand the genetic alphabet of life by designing a strain of E. coli bacteria that creates proteins unlike anything cells can produce naturally.

The technique, detailed in a paper published today in the journal Nature, could lead to the production of totally new types of protein-based medicines, plastics and biofuels.

It could also stretch the definition of natural vs. artificial life.

“I would not call this a new lifeform — but it’s the closest thing anyone has ever made,” study leader Floyd Romesberg, a biochemist at the Scripps Research Institute, said in a news release.

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Fred Hutch’s chief enlists techies to fight cancer

Gary Gillilland
Gary Gilliland, president and director of the Fred Hutchinson Cancer Research Center, stands by his prediction that most cancers will be curable by 2025. (GeekWire Photo / Alan Boyle)

The president and director of Seattle’s Fred Hutchinson Cancer Research Center, Gary Gilliland, is bringing big-data experts on board to make good on his controversial prediction that there could be cures and therapies for “most, if not all, human cancers” by 2025.

Those experts include Microsoft CEO Satya Nadella and Mike Clayville, a vice president at Amazon Web Services, both of whom serve on Fred Hutch’s board of trustees.

Gilliland, one of the featured speakers at the upcoming GeekWire Summit, says “big data is going to be hugely important for the next steps” in the fight against cancer, which will focus on leveraging a huge amount of biological data to personalize cancer treatments.

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Gene editing fixes flaw linked to bad hearts

Embryo editing
This sequence of images shows the development of embryos after co-injection of a gene-correcting enzyme and sperm from a donor with a genetic mutation known to cause a type of heart disease known as hypertrophic cardiomyopathy. (OHSU Photo)

Researchers from Oregon Health and Science University provided the details today on an experiment with human embryos that demonstrated how gene editing can repair a genetic flaw linked to heart disease.

The outlines of the experiment were reported last week, but the OHSU team held off on providing the details until today’s publication of the study in the journal Nature.

The team, led by OHSU senior researcher Shoukhrat Mitalipov, took advantage of a technique known as CRISPR-Cas9, which uses RNA guide molecules and enzymes to make targeted cuts in the DNA molecules that contain the human genetic code. Revised code can then be inserted into the snipped DNA.

The Nature study revealed that the team was able to fix a genetic mutation that causes hypertrophic cardiomyopathy, a common disease that can cause sudden heart failure and death.

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Oregon team edits genes in human embryos

Embryo and pipette
A pipette injects CRISPR-Cas9 gene-editing tools into a mouse embryo. Oregon researchers have reportedly conducted similar experiments using human embryos. (University of Utah Health Sciences Photo)

Chinese researchers crossed a threshold last year when they used CRISPR-Cas9 gene-editing tools to modify human embryos, and now Oregon researchers have reportedly crossed it as well.

A report in MIT Technology Review suggests that the team at Oregon Health and Science University in Portland improved upon the results from China by modifying embryos earlier in their development.

OHSU confirmed that a study was in the works, but said there was nothing more to share at this time.

“Results of the peer-reviewed study are expected to be published soon in a scientific journal,” OHSU spokesman Erik Robinson said in an email to GeekWire.

Genetic experiments with embryos are controversial because they could involve changing the human genetic code in ways that can be passed along to a person’s progeny. That raises the prospect of creating subspecies of genetically modified humans with enhanced traits.

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Genetic code harnessed as digital circuitry

Biologically based circuit NOR gate
An artist’s conception shows connections between biologically based CRISPR-dCas9 NOR gates. (University of Washington Graphic)

Researchers from the University of Washington have taken advantage of synthetic biology to turn yeast cells into building blocks for digital information processing.

The experiment, described today in Nature Communications, turned the cells’ genetic code into NOR logic gates suitable for biologically based circuitry.

In digital circuitry that deals with ones and zeros, a NOR gate will produce a “1” output only if both inputs are “0.” To adapt yeast cells for digital processing, the UW team used a gene-editing method called CRISPR-Cas9 to replicate the interactions of ones and zeros with DNA and RNA molecules.

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Diarrhea linked to telomere troubles later in life

Image: Telomeres
Telomeres, highlighted in green, serve as protective DNA caps for the cell’s chromosomes. (Illustration courtesy of BioViva USA)

Frequent bouts of diarrhea can be bad news for babies, even decades later: A new study has found a correlation between childhood infections and significant shortening of telomeres, a phenomenon that’s linked to the cellular aging process.

The findings, published today in the American Journal of Human Biology, point to a potential linkage between the environmental and genetic factors that play a role in human health.

They also point to the importance of initiatives aimed at curbing infant diarrhea, such as those funded by the Bill & Melinda Gates Foundation.

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Genes edited to create color-coded stem cells

Stem cell
A cluster of human induced pluripotent stem cells contains dyes that highlight cell membranes (purple) and DNA in the nucleus (blue). Spindles from microtubules, shown in white at the center of the image, aid in cell division. (Allen Institute for Cell Science Photo)

Researchers in Seattle have taken advantage of two of the hottest trends in biotech – cell reprogramming and CRISPR/Cas9 gene editing – to create human stem cells that glow as they turn into different tissue types.

The Allen Institute for Cell Science is making the genetically modified cells available to researchers around the world, with the aim of unlocking the secrets behind cell development.

“These are the first five cell lines in a collection of about 20 that we hope to be releasing in the next year,” Susanne Rafelski, the institute’s director of assay development, told GeekWire in advance of today’s unveiling of the Allen Cell Collection.

The institute’s executive director, Rick Horwitz, explained that each of the millions of cells in our body is like a city, with resources that move around from where they’re made to where they’re used.

“With these cell lines, we aim to give the cell science community a kind of live traffic map, to see when and where the parts of the cell are with the clarity and consistency they need to make progress toward understanding human health and tackling disease,” he said in a news release.

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